Database PROSITE

Prosite (http //www.expasy.org/prosite), database of protein domains, families, and functional sites. 

Prosite is perhaps the best known of the domain databases (Hofmann et al., 1999). The Prosite database is a good source of high quality annotation for protein domain families. Prosite documentation includes a section on the functional meaning of a match to the entry and a list of example members of the family. Prosite documentation also includes literature references and cross links to other databases such as the PDB collection of protein structures (Bernstein et al., 1977). For each Prosite document, there is a Prosite pattern, profile, or both to detect the domain family. The profiles are the most sensitive detection method in Prosite. The Prosite profiles provide Zscores for matches allowing statistical evaluation of the match to a new protein. Profiles are now available for many of the common protein domains. Prosite profiles use the generalized profile software (Bucher et al., 1996). 

Hulo, N., Sigrist, C.J. A., LeSaux, V., Langendijk-Genevaux, P. S., Bordoli, L., Gattiker, A., De Castro, E., Bucher, P., and Bairoch, A. (2004). Recent improvements to the PROSITE Database. Nucl. Acids Res. 32, D134-D137. 

PROSITE is a database of biologically significant sites and patterns (amino acid residues) formulated from a known family of proteins as the characteristic familial identifiers or signatures that can be used to detected such family from the query sequences of proteins. If the PROSITE database (prosite.dat downloaded from http //expasy.hcuge.ch/sprot/prosite.html) is installed in the usrstuff directory, selecting Search for PROSITE tool from the Edit menu returns a list of ProSite for... 

PROSITE database http //www.expasy.ch/databases/prostie/... 

The PROSITE database" " of protein sequence motifs is a standard. The motifs are represented by patterns and profiles. Patterns are denoted using the single letter amino acid alphabet, with each position separated by a hyphen, e.g., A-D-E. X is used if any residue is allowed. If several residues are allowed at a given position, they are grouped in square brackets (e.g., [AC]-D-E). Disallowed residues are grouped in curly brackets A-D- FGH. A repeat is indicated by its length after the... 

The primary sequence of a protein also contains the information whether a protein is secreted or which cellular compartment it is destined for. In particular, secretory proteins contain a N-terminal signal peptide for the recognition of which programs have been developed [15]. Other signals like, e.g., nuclear localization signals are notoriously hard to describe. Many posttranslational modifications, on the other hand, are linked to particular amino acid patterns as described in the Prosite database. 

The dual question to the one that assigns related sequences from a database to a given query sequence or family is the question that tries to assign to a query sequence the family that it is a member of or the domains that it contains. One simple yet very effective resource for this purpose is the Prosite database [107, 108] which contains amino acid patterns that are descriptive for particular domains, families, or functions. These patterns allow to specify alternative residues in particular positions or variable length spacers between positions. Matching a sequence against a Prosite entry... 

Hulo, N Bairoch, A., Bulliard, V., et al. (2006) The PROSITE database. Nucl. Acids Res. 34, D227-D230. 

Hulo, N., C. J. Sigrist, V. Le Saux, P. S. Langendijk-Genevaux, L. Bordoli, A. Gattiker, E. De Castro, P Bucher, and A. Bairoch. 2004. Recent improvements to the PROSITE database. Nucleic Acids Res 32, Database Issue D134-7. 

E. De Castro, P Bucher, and A. Bairoch. 2004. Recent improvements to the PROSITE database. Nucleic Acids Res 32 134-7. 

The PROSITE database, maintained by the Swiss Institute of Bioinformatics (SIB), was the first database that tried to catalog functional motifs and domains of proteins1621. Nowadays, PROSITE consists of two major parts storing different types of descriptors the pattern library and the profile library1631. 

The pattern entries of the PROSITE database are based on a regular expression syntax, which emphasises only the most highly conserved residues in a protein family, corresponding approximately to what is termed a conservation pattern in Sect. 5.3. In contrast to the other databases mentioned below, PROSITE patterns do not attempt to describe a complete domain or even protein, but rather try to identify the functionally most important residue combinations, which in enzymes typically correspond to the active site. As an example of the PROSITE syntax, K-x(l,2)-[DEj would mean a lysine residue, followed by one or two arbitrary residues, followed by a residue that is either aspartate or glutamate. When a sequence is compared with a library of such patterns, any pattern is found to be either present or absent, no intermediate scores are assigned. Currently, the PRO SITE pattern libraries contains approximately 1400 entries. 

The PROSITE database is used to determine the domain and the family of the protein sequences that, in turn, are based on biologically significant sites, patterns, and profiles.This database is similar to the HOMologous STRucture Alignment Database " (HOMSTRAD) and the Protein family (Pfam) database, both of which contain domain and family information for proteins. HOMSTRAD uses sequence and structure to group proteins into domains and families. Pfam classifies protein domains and families, based... 

Castro, P. Buchner, and A. Bairoch, Nucleic Acids Res., 32, D134 (2004). Recent Improvements to the PROSITE Database. The PROSITE website http //us.expasy.otg/prosite/. 

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